How to make 2 objects appearing as connected (while remaining separated in the outliner)
The only reason I know of NOT to intermesh objects would be that it may cause complications with modifiers (eg. subsurface modifier).  But for all the hard surface stuff I do, my gosh, 99% of it is objects overlapping eachother. Another solution is the boolean tool. It can union/join objects together so there's no inner/hidden vertecies.